Ktfix3 #6
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Ktfix3 #6
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…ng csq annotation (hail-is#1101)
… lambda (hail-is#1111) * Added statistical functions useful for meta-analysis and genomic control lambda - added pnorm, qnorm, inverseChiSquaredTailOneDF to stats package - added tests to StatsSuite - added pnorm, qnorm, pchisq1tail, qchisq1tail to function registry - added tests to ExprSuite - added docs to HailExpressionLanguage.md * changed C to Z^2
* changed nSmaller to nLess for histograms * fixed formatting and docs * changed gqDensities to gqHist
…-is#1085) * Fix python methods, expose samples_to_pandas * Better logging support * More better * made exception handling messages private * fix tests * call configure from main * Address comments * Added configure to tests * Fix bgzip test
- takes in a named expression specifying the keys of the new table - takes named aggregator expressions specifying how the columns should be computed
Now both aggregate and aggregateRows KT tests pass.
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* Reference Genome #6: Type fixes * fixed test * Addressed comments * addressed comments * addressed comments
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* # This is a combination of 22 commits. # This is the 1st commit message: apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue # This is the commit message #2: convert relational.scala ; # This is the commit message #3: scope the extract aggregators constfb call # This is the commit message #4: scope interpret # This is the commit message #5: typeAfterSelect used by selectRegionValue # This is the commit message #6: load matrix # This is the commit message #7: imports # This is the commit message #8: loadbgen converted # This is the commit message #9: convert loadplink # This is the commit message hail-is#10: convert loadgdb # This is the commit message hail-is#11: convert loadvcf # This is the commit message hail-is#12: convert blockmatrix # This is the commit message hail-is#13: convert filterintervals # This is the commit message hail-is#14: convert ibd # This is the commit message hail-is#15: convert a few methods # This is the commit message hail-is#16: convert split multi # This is the commit message hail-is#17: convert VEP # This is the commit message hail-is#18: formatting fix # This is the commit message hail-is#19: add partitionBy and values # This is the commit message hail-is#20: fix bug in localkeysort # This is the commit message hail-is#21: fixup HailContext.readRowsPartition use # This is the commit message hail-is#22: port balding nichols model * apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue convert relational.scala ; scope the extract aggregators constfb call scope interpret typeAfterSelect used by selectRegionValue load matrix imports loadbgen converted convert loadplink convert loadgdb convert loadvcf convert blockmatrix convert filterintervals convert ibd convert a few methods convert split multi convert VEP formatting fix add partitionBy and values fix bug in localkeysort fixup HailContext.readRowsPartition use port balding nichols model port over table.scala couple fixes convert matrix table remove necessary use of rdd variety of fixups wip add a clear * Remove direct Region allocation from FilterColsIR When regions are off-heap, we can allow the globals to live in a separate, longer-lived Region that is not cleared until the whole partition is finished. For now, we pay the memory cost. * Use RVDContext in MatrixRead zip This Region will get cleared by consumers. I introduced the zip primitive which is a safer way to zip two RVDs because it does not rely on the user correctly clearing the regions used by the left and right hand sides of the zip. * Control the Regions in LoadGDB I do not fully understand how LoadGDB is working, but a simple solution to the use-case is to serialize to arrays of bytes and parallelize those. I realize there is a proliferation of `coerce` methods. I plan to trim this down once we do not have RDD and ContextRDD coexisting * wip * unify RVD.run * reset in write * fixes * use context region when allocating * also read RVDs using RVDContext * formatting * address comments * remove unused val * abstract over boundary * little fixes * whoops forgot to clear before persisting This fixes the LDPrune if you dont clear the region things go wrong. Not sure what causes that bug. Maybe its something about encoders? * serialize for shuffles, region.scoped in matrixmapglobals, fix joins * clear more! * wip * wip * rework GeneralRDD to ease ContextRDD transition * formatting * final fixes * formatting * merge failures * more bad merge stuff * formatting * remove unnecessary stuff * remove fixme * boom! * variety of merge mistakes * fix destabilize bug * add missing newline * remember to clear the producer region in localkeysort * switch def to val * cleanup filteralleles and exporbidbimfam * fix clearing and serialization issue * fix BitPackedVectorView Previously it always assumed the variant struct started at offset zero, which is not true * address comments, remove a comment * remove direct use of Region * oops * werrrks, mebbe * needs cleanup * fix filter intervals * fixes * fixes * fix filterintervals * remove unnecessary copy in TableJoin * and finally fix the last test * re-use existing CodecSpec definition * remove unnecessary boundaries * use RVD abstraction when possible * formatting * bugfix: RegionValue must know its region * remove unnecessary val and comment * remove unused methods * eliminate unused constructors * undo debug change * formatting * remove unused imports * fix bug in tablejoin * fix RichRDDSuite test If you have no data, then you have no partitions, not 1 partition
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Rebased hail-is/master.